Xiaojing Yang

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Name: Yang, Xiaojing
Organization: University of Illinois at Chicago , USA
Department:
Title: Assistant(PhD)
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Photochemistry and Photobiology 2017 Volume 93(Issue 1) pp:304-314
Publication Date(Web):2017/01/01
DOI:10.1111/php.12699
AbstractPhrB from Agrobacterium fabrum is the first prokaryotic photolyase which repairs (6-4) UV DNA photoproducts. The protein harbors three cofactors: the enzymatically active FAD chromophore, a second chromophore, 6,7-dimethyl-8-ribityllumazine (DMRL) and a cubane-type Fe-S cluster. Tyr424 of PhrB is part of the DNA-binding site and could provide an electron link to the Fe-S cluster. The PhrBY424F mutant showed reduced binding of lesion DNA and loss of DNA repair. The mutant PhrBI51W is characterized by the loss of the DMRL chromophore, reduced photoreduction and reduced DNA repair capacity. We have determined the crystal structures of both mutants and found that both mutations only affect local protein environments, whereas the overall fold remained unchanged. The crystal structure of PhrBY424F revealed a water network extending to His366, which are part of the lesion-binding site. The crystal structure of PhrBI51W shows how the bulky Trp leads to structural rearrangements in the DMRL chromophore pocket. Spectral characterizations of PhrBI51W suggest that DMRL serves as an antenna chromophore for photoreduction and DNA repair in the wild type. The energy transfer from DMRL to FAD could represent a phylogenetically ancient process.
Co-reporter:Xiaojing Yang;Sherwin Montano;Zhong Ren
Photochemistry and Photobiology 2015 Volume 91( Issue 5) pp:993-1003
Publication Date(Web):
DOI:10.1111/php.12470

Abstract

UVR8 is the only known plant photoreceptor that mediates light responses to UV-B (280–315 nm) of the solar spectrum. UVR8 perceives a UV-B signal via light-induced dimer dissociation, which triggers a wide range of cellular responses involved in photomorphogenesis and photoprotection. Two recent crystal structures of Arabidopsis thaliana UVR8 (AtUVR8) have revealed unusual clustering of UV-B-absorbing Trp pigments at the dimer interface and provided a structural framework for further mechanistic investigation. This review summarizes recent advances in spectroscopic, computational and crystallographic studies on UVR8 that are directed toward full understanding of UV-B perception at the molecular level.

Co-reporter:Xuefei Yang;Xiaoli Zeng;Keith Moffat
Acta Crystallographica Section F 2015 Volume 71( Issue 10) pp:1215-1222
Publication Date(Web):
DOI:10.1107/S2053230X15014661

Two-component signal transduction is the major signaling mechanism that enables bacteria to survive and thrive in complex environmental conditions. The photosynthetic bacterium R. palustris employs two tandem bacteriophytochromes, RpBphP2 and RpBphP3, to perceive red-light signals that regulate the synthesis of light-harvesting complexes under low-light conditions. Both RpBphP2 and RpBphP3 are photosensory histidine kinases coupled to the same response regulator RPA3017. Together, they constitute a two-component system that converts a red-light signal into a biological signal. In this work, the crystal structure of RPA3017 in the unphosphorylated form at 1.9 Å resolution is presented. This structure reveals a tightly associated dimer arrangement that is conserved among phytochrome-related response regulators. The conserved active-site architecture provides structural insight into the phosphotransfer reaction between RpBphP2/RpBphP3 and RPA3017. Based on structural comparisons and homology modeling, how specific recognition between RpBphP2/RpBphP3 and RPA3017 is achieved at the molecular level is further explored.

Co-reporter:Xiaojing Yang, Emina A. Stojković, Wesley B. Ozarowski, Jane Kuk, ... Keith Moffat
Structure (7 July 2015) Volume 23(Issue 7) pp:1179-1189
Publication Date(Web):7 July 2015
DOI:10.1016/j.str.2015.04.022
•RpBphP2 and RpBphP3 adopt similar tertiary structures but different dimer scaffolds•Residues at the GAF-PHY interface modulate photoconversion properties•A single mutation (T480P) in RpBphP3 enables canonical photoconversion•Angular orientation between PHY and HK domains is crucial for long-range signalingRpBphP2 and RpBphP3, two tandem bacteriophytochromes from the photosynthetic bacterium Rhodopseudomonas palustris, share high sequence identity but exhibit distinct photoconversion behavior. Unlike the canonical RpBphP2, RpBphP3 photoconverts to an unusual near-red-absorbing (Pnr) state; both are required for synthesis of light-harvesting complexes under low-light conditions. Here we report the crystal structures of the photosensory core modules of RpBphP2 and RpBphP3. Despite different quaternary structures, RpBphP2 and RpBphP3 adopt nearly identical tertiary structures. The RpBphP3 structure reveals tongue-and-groove interactions at the interface between the GAF and PHY domains. A single mutation in the PRxSF motif at the GAF-PHY interface abolishes light-induced formation of the Pnr state in RpBphP3, possibly due to altered structural rigidity of the chromophore-binding pocket. Structural comparisons suggest that long-range signaling involves structural rearrangement of the helical spine at the dimer interface. These structures, together with mutational studies, provide insights into photoconversion and the long-range signaling mechanism in phytochromes.Download high-res image (143KB)Download full-size image
Phytochrome